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Detailed information for vg0217154297:

Variant ID: vg0217154297 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17154297
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGATACGTTAAGGGAGAATAGCCACTATGGTCCCTGAAGTTTCGCTCTGAGATCGTTTTAGCCCCTGACCTTTCAAATTGTCTAAGCAAGCCCTTAAACT[T/C]
TATCATGTGGGCATATATAGTCCTTGGCCCATCGAAAATTGCCACGTGGGCATGTCATGTCATCTTCCAATGCAAATATATGATGAAATACCCAATTTAC

Reverse complement sequence

GTAAATTGGGTATTTCATCATATATTTGCATTGGAAGATGACATGACATGCCCACGTGGCAATTTTCGATGGGCCAAGGACTATATATGCCCACATGATA[A/G]
AGTTTAAGGGCTTGCTTAGACAATTTGAAAGGTCAGGGGCTAAAACGATCTCAGAGCGAAACTTCAGGGACCATAGTGGCTATTCTCCCTTAACGTATCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 5.00% 0.28% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 84.70% 14.50% 0.86% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 58.30% 39.10% 2.58% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0217154297 T -> C LOC_Os02g28970.1 downstream_gene_variant ; 1765.0bp to feature; MODIFIER silent_mutation Average:52.98; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0217154297 T -> C LOC_Os02g28980.1 downstream_gene_variant ; 2133.0bp to feature; MODIFIER silent_mutation Average:52.98; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0217154297 T -> C LOC_Os02g28970.2 downstream_gene_variant ; 482.0bp to feature; MODIFIER silent_mutation Average:52.98; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0217154297 T -> C LOC_Os02g28970-LOC_Os02g28980 intergenic_region ; MODIFIER silent_mutation Average:52.98; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217154297 NA 5.76E-06 mr1047 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 2.48E-06 mr1471 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 9.40E-06 mr1502 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 1.85E-07 mr1543 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 2.87E-06 mr1642 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 2.84E-06 2.84E-06 mr1815 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 4.46E-06 mr1990 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0217154297 NA 2.62E-07 mr1850_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251